Updated the page on the web site with the new script.
Figured it out; if you pass the parameter -label_position 'left' it
will display the label to the left. However it displays them right
next to the segment (ala GBrowse). I added a hack to
Bio::Graphics::Glyph::generic in CVS which allows 'alignment_left' as
an option, displaying it aligned to the far left of the panel; there
is probably a way to use a callback here as well.
chris
On Sep 5, 2007, at 8:31 AM, Albert Vilella wrote:
> Awesome!!
>> Thanks Chris!
>> On 9/5/07, Chris Fields <cjfields at uiuc.edu> wrote:
>>>> You mean something like this?
>>>>http://www.bioperl.org/wiki/HOWTO_Discussion:Graphics>>>> chris
>>>> On Sep 5, 2007, at 4:42 AM, Albert Vilella wrote:
>>>>> A couple of examples:
>>>>>>http://www.treefam.org/cgi-bin/alnview.pl?ac=TF105041>>>>>> treefam has exon boundary and PFAM domain mappings
>>>>>>http://www.ensembl.org/Homo_sapiens/genetreeview?>>> gene=ENSG00000139618
>>>>>> here the tree is shown as well, but the idea would be to plot the
>>> alignment
>>>>>> So it's more "show me the multiple CDS/protein alignment" rather
>>> than "show
>>> my aligned CDS/proteins wrt my reference genome"
>>>>>> I think it would be quite neat to have this as a bioperl howto,
>>>>>> Comments?
>>>>>> Albert.
>>>>>> On 9/4/07, Chris Fields <cjfields at uiuc.edu> wrote:
>>>>>>>>>>>> On Sep 4, 2007, at 9:31 AM, Jay Hannah wrote:
>>>>>>>>> On Aug 31, 2007, at 4:29 AM, Albert Vilella wrote:
>>>>>> Probably a bit of a long shot but does anyone have code for
>>>>>> displaying protein or CDS multiple sequence alignments with the
>>>>>> exon
>>>>>> boundaries of each gene in the alignment?
>>>>>>>>>>>> Something in the bioperl world without funky external
>>>>>> dependencies.
>>>>>> I think
>>>>>> it would be an awesome addition to the howtos.
>>>>>>>>>>>> Currently, the Bio::Graphics howto has cdna to genome mapping
>>>>>> scripts or
>>>>>> blast output scripts, but
>>>>>> I couldn't find code for dealing with multiple sequence
>>>>>> alignments.
>>>>>>>>>> I'm currently under the (potentially uninformed) impression that
>>>>> Bio::Graphics and related tools only work with a single
>>>>> coordinate
>>>>> system. I've never seen a multiple sequence alignment example.
>>>>>>>>>> (
>>>>> I Google'd for "gbrowse alignment" and hit this:
>>>>>http://maizeapache.danforthcenter.org/cgi-bin/gbrowse.cgi>>>>>>>>>> Click the second Example link and you'll see exons mapped out.
>>>>>>>>>> But zooming all the way in with all the tracks turned on it
>>>>> looks
>>>>> like the AZM tracks are just the coding regions. I don't see any
>>>>> multiple sequence alignment...
>>>>> )
>>>>>>>>>> I doubt that helped. :)
>>>>>>>>>> Jay Hannah
>>>>>http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah>>>>>>>> Acc. to the Gbrowse tutorial GBrowse can deal with alignment data:
>>>>>>>>http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome->>>> Browser/docs/tutorial/tutorial.html
>>>>>>>> chris
>>>>>>>> _______________________________________________
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>>>>Bioperl-l at lists.open-bio.org>>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l>>>>>>> _______________________________________________
>>> Bioperl-l mailing list
>>>Bioperl-l at lists.open-bio.org>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l>>>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>>>>>>>> _______________________________________________
> Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org>http://lists.open-bio.org/mailman/listinfo/bioperl-l
Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign